AST 248, Lecture 10
James Lattimer
Department of Physics & Astronomy
449 ESS Bldg.
Stony Brook University
April 1, 2016
The Search for Intelligent Life in the Universe
james.lattimer@stonybrook.edu
James Lattimer
AST 248, Lecture 10
Abundances of the Elements
Element
H
He
O
C
N
Ne
Mg
Si
Fe
S
Al
Ca
Na
Ni
Cr
P
Stars &
Universe
93.4
6.5
0.06
0.03
0.011
0.01
0.003
0.003
0.002
0.001
0.0002
0.0002
0.0002
0.0001
0.00004
0.00003
Earth
Crust
0.14
0
47
0005
0.0003
0
2.1
28
5
0.026
8.1
3.6
2.8
0.1
0
0.1
Earth
Ocean
66.2
0
33.1
0.001
0
0
0.03
0
0
0.017
0
0
0
0
0
0
James Lattimer
Life
61
0
26
10.5
2.4
0
0.011
0
0.01
0.13
0
0.23
0.01
0
0
0.13
AST 248, Lecture 10
Composition of Biological Compounds
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Organisms are made from long chains of monomers called polymers.
A monomer is a molecule made from individual atoms.
An atom is one of the approximately 100 stable elements, or which 4
are ultra-important and 2 more are moderately important.
Element # bonds Element # bonds Element # bonds
H
1
C
4
N
3
O
2
P
5
S
2
The number of bonds are the maximum number of covalent bonds
elements can form. A covalent bond is formed when electrons are
shared among atoms.
Even though some elements can share
more electrons, e.g., P, C has the
most flexibility in forming molecules
of different shapes and sizes.
Most molecules that are carbon-based
are called organic molecules and can
be very complex. Elemental carbon,
cabonates, CO2 and cyanides are
considered inorganic.
James Lattimer
AST 248, Lecture 10
Major Types of Organic Biological Molecules
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Lipids (fats and oils) – although polar, are poorly soluble in water, so they
are not found as individual molecules but weakly bonded aggregates
or macromolecules. They store energy and are useful in membranes.
Carbohydrates – polar, soluble, molecules with many OH hydroxyl groups
attached. Sugars are ring-like carbohydrates, polysaccharides are
linear or branched networks of carbohydrates. Carbohydrates store
energy and provide structural support.
Proteins – most complex macromolecules found, linear trains of amino
acids. Like polysaccharides, they polymerize by releasing water.
Provide structure and act as catalysts (called enzymes).
Nucleic Acids – Largest macromolecules found, are collections of
individual nucleotides linked into linear polymers. Each nucleotide
consists of one sugar, one nitrogeneous base and one or more
phosphate groups. Examples: DNA and RNA.
James Lattimer
AST 248, Lecture 10
Isomers and Chirality
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When larger groups of atoms are assembled, there may be multiple
ways to bond the same number of atoms. Each of the different ways
is called an isomer.
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Some isomers show handedness: these are called stereoisomers and
are either left- or right-handed. They are mirror images of each
other. In general, life utilizes only one handedness (e.g., left-handed
amino acids are used to make proteins).
James Lattimer
AST 248, Lecture 10
Carbon Isomers and Chirality
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Chirality is the quality that makes handedness unique.
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If less than 4 different things are linked to the central carbon, the
molecule is achiral.
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If 4 different things are linked to the central carbon, the molecule is
chiral.
James Lattimer
AST 248, Lecture 10
Handedness
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Humans are 9:1 right-handed, but terrestrial biochemistry contains only
left-handed amino acids.
Meteorites contain amino acids in nearly equal proportions of left- and
right-handed varieties. The ratio is left:right = 1.08:1, and no one
know why. One possible explanation has to do with circularly
polarized UV light in the stellar association where the Sun formed,
as is observed in the Orion nebula.
Left-and right-handed molecules can have very different properties.
Drugs especially can be affected. Some examples are:
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Orange and lemon peels get aromas from limonene, but it is left-handed in
oranges and right-handed in lemons, which obviously smell different.
The molecule carvone makes the smells of mint (left) and caraway (right).
The drug ibuprofen, if left-handed, is 4 times as strong as the other kind.
The sedative Darvon is an isomer of the cough medicine ingredient Novrad.
The drug thalidomide is used to control morning sickness, but its mirror
image causes birth defects.
Ethambutol: one handedness is used to treat tuberculosis, the other causes
blindness.
Naproxen: one handedness is used to treat arthritis, but the other causes
liver poisoning.
Molecular activity can also be affected by handedness. Penicillin kills
only bacteria in cell walls but not the cells themselves because of
handedness.
James Lattimer
AST 248, Lecture 10
Building Blocks and Selectivity
The largest organic molecules are polymers, or long chains of
monomers, which often containing repeating units or patterns.
I One could view monomers as lego blocks: an infinite variety are
possible, but only a select few are actually used.
I Monomers tend to be simple, because otherwise it might be too
difficult or take too long to form them, either deliberately or by
chance.
I Examples: there are 35 isomers of C9 H20 and 60 trillion isomers of
C40 H82 .
I Example of selectivity: About 20 different amino acids are found in
living material although virtually billions are possible to be formed in
the laboratory.
I Another example: Proteins are made of chains of about 100 amino
acids. About 20 different amino acids are used. About 100,000
different proteins found in living material although it is possible to
form 119!/(100!19!) = 5 · 1021 combinations.
I Selectivity is extended by utilizing only a single handedness.
Kinds of polymers and their monomers:
I proteins – amino acids
I carbohydrates – sugars
I nucleic acids – bases, sugars, phosphates
I lipids – fatty acids
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James Lattimer
AST 248, Lecture 10
Major Domains of Life
Based on rRNA data, proposed by C. Woese
Eric Gaba, NASA
James Lattimer
AST 248, Lecture 10
Other Groupings
James Lattimer
AST 248, Lecture 10
Differences Between Archaea and Bacteria
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Bacteria and Archaea both have 70S ribosomes, but have different
ribosomal RNA (rRNA) shapes.
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Bacteria and Archaea have different types of cell walls.
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Archaea have 3 RNA polymerases like eukaryotes and their
ribosomes work more like eukaryotes.
Bacteria have only 1 RNA polymerase.
Bacteria have cell walls containing peptiodoglycan.
Archaea have cell walls lacking peptiodoglycan.
Bacteria
and Archae have different cell membranes.
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Bacteria have cell membranes with ester bonds.
Archae have cell membranes with ether bonds which enclose lipids
with hydrocarbons rather than fatty acids. Monolayers and histones
enhance DNA stability.
Archaea
Bacteria
bi- lipid layers
Bacteria
monoArchaea
James Lattimer
AST 248, Lecture 10
Types of Cells
Prokaryotes Cells without nuclei
Eukaryotes Cells with nuclei
Viruses
Major Differences:
I Prokaryotes form bacteria domains
eubacteria and archaea.
I Prokaryotes form single-celled organisms, but can cluster into colonies. Mariana Ruiz
I Euacteria are enclosed by cell walls made of cross-linked peptidoglycan
chains (amino acids + sugar) which maintains size and shape of cell.
I Metabolism in prokaryotes is complex and more diverse.
I Prokaryotic genome is smaller, and its DNA is not attached to histone
proteins.
I Most prokaryotic DNA is present in a single circular chromosome, and
replication begins at a single point and proceeds around the circle in
both directions.
I Prokaryotes obtain new genes by conjugation (transferral),
transformation (absorbed from environment) and transduction
(transferral by viruses or phages.
I Ribosomes of eubacteria differ in molecular detail from those of
eukaryotes and archaea prokaryotes.
James Lattimer
AST 248, Lecture 10
Metabolism
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Chemical processses that provide energy
and nutrients to cells. Without cell’s
presence, these reactions would occur too
slowly to be useful. Cell’s primary
purpose is to speed up these reactions.
Metabolism requires both sources of
raw materials and energy to break
down old molecules and
manufacture new ones.
Cells produce a large variety
of products from a very
limited set of starting
materials, utilizing a
diverse array of enzymes.
Regardless of where energy
comes from, cells utilize
the same molecule (ATP,
adenosine triphosphate)
to store and release
energy. ATP is
completely recyclable.
James Lattimer
hyperphysics.phy-astr.gsu.edu/hbase/biology
AST 248, Lecture 10
Metabolic Sources
Carbon sources
Heterotroph Organism which gets its carbon by eating (animals, many
microscopic organisms)
Autotroph Organism which gets its carbon from CO2 in the
atmosphere or dissolved in water (most plants)
Energy sources
Sunlight (photosynthesis) photoOrganic (food) chemoI Inorganic (chemicals) chemoMetabolic class
Carbon source
Energy source
photoautotroph
CO2
sunlight
chemoautotroph
CO2
inorganic chemicals (e.g., Fe, S, NH3 )
photoheterotroph
organic compounds
sunlight
chemoheterotroph organic compounds
organic compounds
Metabolic class
Examples
photoautotroph
plants, photosynthetic bacteria
chemoautotroph
extremophile archaea and bacteria
photoheterotroph
some bacteria and archaea
chemoheterotroph
animals, many microbes
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James Lattimer
AST 248, Lecture 10
Metabolism and the Implications for Life
Cell structures are a probable basis for extraterrestrial life.
I General nature of metabolic classes implies they apply to
extraterrestrial life.
I Any type of complex metabolism requires existence of
some kind of structure that allows carbon and energy to
come together and manufacture or break down molecules.
Water plays key roles and might be universally required.
I Water is a polar solvent, opposite sides have opposite
charges.
I Organic chemicals are readily available for reactions by
being dissolved in water if they are polar (hydrophilic as
opposed to hydrophobic).
I Water provides the medium
for transporting chemicals to
and within cells and transporting waste products away.
I Water is essential in cellular
metabolic reactions, such as
the ATP-ADP cycle.
James Lattimer
AST 248, Lecture 10